RNAsmc

RNAsmc detects and quantitatively compares RNA secondary structure (RSS) motifs to characterize structural heterogeneity and functional variation.

Key Features:

• Structural Motif Detection and Quantification: Identifies RSS motifs, scores similarity among structural components, and quantifies variations associated with single nucleotide variants (SNVs), single nucleotide polymorphisms (SNPs), insertions, and deletions.
• Robust Comparative Analysis: Maintains performance across variable sequence lengths, folding protocols, and chemical probing–derived structural profiles, enabling detection of RiboSNitches and evaluation of allosteric effects.

Scientific Applications:

• RNA Family Clustering and Functional Analysis: Clusters RNA families based on structural heterogeneity and assesses structure–function relationships in gene regulation and RNA stability.

Methodology:

RNAsmc applies a dynamic alignment framework to compare RSS motifs across sequences, enabling precise structural similarity scoring and clustering despite sequence variability and experimental noise.